BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 044054
(400 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1EG7|A Chain A, The Crystal Structure Of Formyltetrahydrofolate Synthetase
From Moorella Thermoacetica
pdb|1EG7|B Chain B, The Crystal Structure Of Formyltetrahydrofolate Synthetase
From Moorella Thermoacetica
Length = 557
Score = 218 bits (554), Expect = 6e-57, Method: Compositional matrix adjust.
Identities = 145/393 (36%), Positives = 194/393 (49%), Gaps = 78/393 (19%)
Query: 14 SPVPADIDIANSVEPLHISEIAQELNLKPNHYDLYGKYKAKVLLSVLDELEGSADGYYVV 73
S VP+DI+IA + + + E+A+ L ++ + +LYGKYKAK+ L V L+ DG ++
Sbjct: 2 SKVPSDIEIAQAAKMKPVMELARGLGIQEDEVELYGKYKAKISLDVYRRLKDKPDGKLIL 61
Query: 74 VGEITRTPLGEGEITQYPLGEGKSTTTVGLCQALGAFLDKKVVTCLRQPLQGPTFGIRXX 133
V IT T P GEGK+TT+VGL AL A L K+V+ CLR+P GP+FGI+
Sbjct: 62 VTAITPT----------PAGEGKTTTSVGLTDAL-ARLGKRVMVCLREPSLGPSFGIKGG 110
Query: 134 XXXXXYSQVIPMDEFNLHLTGDIHXXXXXXXXXXXXXXXRIFHEASQSDKALFNRLCPPN 193
Y+QV+PM++ NLH TGDIH + Q L P
Sbjct: 111 AAGGGYAQVVPMEDINLHFTGDIHAVTYAHNLLAAMVDNHL-----QQGNVLN---IDPR 162
Query: 194 KEGERSFSNIMFRRLRKLGISKTKPEDLTPEEINRFARLDIDPAS------ITWRRVMDV 247
R ++ R LR + I + P E DI AS +MD+
Sbjct: 163 TITWRRVIDLNERALRNIVIGLGGKANGVPRETG----FDISVASEVMACLCLASDLMDL 218
Query: 248 NDRFLRKITIGQGPEEKGMVRETGFDISVASEIMAVLALTTSLADTRERVGKMVIGNSKA 307
+RF RK+ +G +
Sbjct: 219 KERFSRKV----------------------------------------------VGYTYD 232
Query: 308 GDPITADDLGVGGALTVLMKDAINPTLMQTLEGTPVLVHAGPFANIAHGNSSIVADKIAL 367
G P+TA DL G++ +LMKDAI P L+QTLE TP +H GPFANIAHG +SI+A K AL
Sbjct: 233 GKPVTAGDLEAQGSMALLMKDAIKPNLVQTLENTPAFIHGGPFANIAHGCNSIIATKTAL 292
Query: 368 KLVGPGGIVVTEAGFGADIGAEKFMNIKCRYSG 400
KL VVTEAGFGAD+GAEKF ++KCRY+G
Sbjct: 293 KL---ADYVVTEAGFGADLGAEKFYDVKCRYAG 322
>pdb|1FPM|A Chain A, Monovalent Cation Binding Sites In
N10-formyltetrahydrofolate Synthetase From Moorella
Thermoacetica
pdb|1FPM|B Chain B, Monovalent Cation Binding Sites In
N10-formyltetrahydrofolate Synthetase From Moorella
Thermoacetica
pdb|1FP7|A Chain A, Monovalent Cation Binding Sites In
N10-Formyltetrahydrofolate Synthetase From Moorella
Thermoacetica
pdb|1FP7|B Chain B, Monovalent Cation Binding Sites In
N10-Formyltetrahydrofolate Synthetase From Moorella
Thermoacetica
pdb|3PZX|A Chain A, Native Crystal Structure Of N10-Formyltetrahydrofolate
Synthetase
pdb|3PZX|B Chain B, Native Crystal Structure Of N10-Formyltetrahydrofolate
Synthetase
pdb|3QB6|A Chain A, Crystal Strucutre Of N10-Formyltetrahydrofolate Synthetase
With Folate
pdb|3QB6|B Chain B, Crystal Strucutre Of N10-Formyltetrahydrofolate Synthetase
With Folate
pdb|3RBO|A Chain A, Crystal Structure Of N10-Formyltetrahydrofolate Synthetase
With Adp And Formylphosphate
pdb|3RBO|B Chain B, Crystal Structure Of N10-Formyltetrahydrofolate Synthetase
With Adp And Formylphosphate
pdb|3SIN|A Chain A, Crystal Strucutre Of N10-Formyltetrahydrofolate Synthetase
With Zd9331 And Formylphosphate
pdb|3SIN|B Chain B, Crystal Strucutre Of N10-Formyltetrahydrofolate Synthetase
With Zd9331 And Formylphosphate
pdb|3QUS|A Chain A, Crystal Strucutre Of N10-Formyltetrahydrofolate Synthetase
With Atpgs
pdb|3QUS|B Chain B, Crystal Strucutre Of N10-Formyltetrahydrofolate Synthetase
With Atpgs
Length = 557
Score = 211 bits (537), Expect = 6e-55, Method: Compositional matrix adjust.
Identities = 102/169 (60%), Positives = 127/169 (75%), Gaps = 3/169 (1%)
Query: 232 LDIDPASITWRRVMDVNDRFLRKITIGQGPEEKGMVRETGFDISVASEIMAVLALTTSLA 291
L+IDP +ITWRRV+D+NDR LR I IG G + G+ RETGFDISVASE+MA L L + L
Sbjct: 157 LNIDPRTITWRRVIDLNDRALRNIVIGLGGKANGVPRETGFDISVASEVMACLCLASDLM 216
Query: 292 DTRERVGKMVIGNSKAGDPITADDLGVGGALTVLMKDAINPTLMQTLEGTPVLVHAGPFA 351
D +ER ++V+G + G P+TA DL G++ +LMKDAI P L+QTLE TP +H GPFA
Sbjct: 217 DLKERFSRIVVGYTYDGKPVTAGDLEAQGSMALLMKDAIKPNLVQTLENTPAFIHGGPFA 276
Query: 352 NIAHGNSSIVADKIALKLVGPGGIVVTEAGFGADIGAEKFMNIKCRYSG 400
NIAHG +SI+A K ALKL VVTEAGFGAD+GAEKF ++KCRY+G
Sbjct: 277 NIAHGCNSIIATKTALKL---ADYVVTEAGFGADLGAEKFYDVKCRYAG 322
Score = 121 bits (304), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 65/144 (45%), Positives = 91/144 (63%), Gaps = 11/144 (7%)
Query: 14 SPVPADIDIANSVEPLHISEIAQELNLKPNHYDLYGKYKAKVLLSVLDELEGSADGYYVV 73
S VP+DI+IA + + + E+A+ L ++ + +LYGKYKAK+ L V L+ DG ++
Sbjct: 2 SKVPSDIEIAQAAKMKPVMELARGLGIQEDEVELYGKYKAKISLDVYRRLKDKPDGKLIL 61
Query: 74 VGEITRTPLGEGEITQYPLGEGKSTTTVGLCQALGAFLDKKVVTCLRQPLQGPTFGIRXX 133
V IT T P GEGK+TT+VGL AL A L K+V+ CLR+P GP+FGI+
Sbjct: 62 VTAITPT----------PAGEGKTTTSVGLTDAL-ARLGKRVMVCLREPSLGPSFGIKGG 110
Query: 134 XXXXXYSQVIPMDEFNLHLTGDIH 157
Y+QV+PM++ NLH TGDIH
Sbjct: 111 AAGGGYAQVVPMEDINLHFTGDIH 134
>pdb|3DO6|A Chain A, Crystal Structure Of Putative Formyltetrahydrofolate
Synthetase (Tm1766) From Thermotoga Maritima At 1.85 A
Resolution
pdb|3DO6|B Chain B, Crystal Structure Of Putative Formyltetrahydrofolate
Synthetase (Tm1766) From Thermotoga Maritima At 1.85 A
Resolution
Length = 543
Score = 167 bits (424), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 86/169 (50%), Positives = 108/169 (63%), Gaps = 3/169 (1%)
Query: 232 LDIDPASITWRRVMDVNDRFLRKITIGQGPEEKGMVRETGFDISVASEIMAVLALTTSLA 291
L ID + W+R D NDR LR I IG G G RE F I+ ASE+ A+LAL+ +
Sbjct: 143 LKIDITRVFWKRTXDXNDRALRSIVIGLGGSANGFPREDSFIITAASEVXAILALSENXK 202
Query: 292 DTRERVGKMVIGNSKAGDPITADDLGVGGALTVLMKDAINPTLMQTLEGTPVLVHAGPFA 351
D +ER+GK+++ + DLG+ GA VL+KDAINP L+QT EGTP L+H GPFA
Sbjct: 203 DLKERLGKIIVALDADRKIVRISDLGIQGAXAVLLKDAINPNLVQTTEGTPALIHCGPFA 262
Query: 352 NIAHGNSSIVADKIALKLVGPGGIVVTEAGFGADIGAEKFMNIKCRYSG 400
NIAHG +SI+A K A KL VTEAGFGAD+GAEKF++ R G
Sbjct: 263 NIAHGTNSIIATKXAXKL---SEYTVTEAGFGADLGAEKFIDFVSRVGG 308
Score = 81.6 bits (200), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 52/127 (40%), Positives = 68/127 (53%), Gaps = 11/127 (8%)
Query: 31 ISEIAQELNLKPNHYDLYGKYKAKVLLSVLDELEGSADGYYVVVGEITRTPLGEGEITQY 90
I EIA +L LK + YG Y AK+ L LE DG ++V +T TP GEG
Sbjct: 5 IKEIADQLELKDDILYPYGHYIAKIDHRFLKSLENHEDGKLILVTAVTPTPAGEG----- 59
Query: 91 PLGEGKSTTTVGLCQALGAFLDKKVVTCLRQPLQGPTFGIRXXXXXXXYSQVIPMDEFNL 150
K+TT++GL +L K +VT LR+P GPT G++ S+V+P DE NL
Sbjct: 60 -----KTTTSIGLSXSLNRIGKKSIVT-LREPSLGPTLGLKGGATGGGRSRVLPSDEINL 113
Query: 151 HLTGDIH 157
H TGD H
Sbjct: 114 HFTGDXH 120
>pdb|2EO2|A Chain A, Solution Structure Of The Insertion Region (510-573) Of
Fthfs Domain From Mouse Methylenetetrahydrofolate
Dehydrogenase (Nadp+ Dependent) 1-Like Protein
Length = 71
Score = 79.3 bits (194), Expect = 3e-15, Method: Composition-based stats.
Identities = 38/64 (59%), Positives = 47/64 (73%), Gaps = 1/64 (1%)
Query: 179 SQSDKALFNRLCPPNKEGERSFSNIMFRRLRKLGISKTKPEDLTPEEINRFARLDIDPAS 238
+Q+DKAL+NRL P G R FS I RL+KLGI KT P LT EE+ +FARL+IDPA+
Sbjct: 9 TQTDKALYNRLVPL-VNGVREFSEIQLSRLKKLGIHKTDPSTLTEEEVRKFARLNIDPAT 67
Query: 239 ITWR 242
ITW+
Sbjct: 68 ITWQ 71
>pdb|1V5C|A Chain A, The Crystal Structure Of The Inactive Form Chitosanase
From Bacillus Sp. K17 At Ph3.7
pdb|1V5D|A Chain A, The Crystal Structure Of The Active Form Chitosanase
From Bacillus Sp. K17 At Ph6.4
pdb|1V5D|B Chain B, The Crystal Structure Of The Active Form Chitosanase
From Bacillus Sp. K17 At Ph6.4
Length = 386
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 13/77 (16%)
Query: 15 PVPADIDIANSVEPLHISEIAQELNLKPNHYDLYGKYKAKVLLSVLDELEGSADGYYVVV 74
P P ++ A ++P H+++ + LN Y Y +K K L + L L G GYY V
Sbjct: 6 PFPQQVNYAGVIKPNHVTQ--ESLNASVRSY--YDNWKKKYLKNDLSSLPG---GYY-VK 57
Query: 75 GEIT-----RTPLGEGE 86
GEIT PLG E
Sbjct: 58 GEITGDADGFKPLGTSE 74
>pdb|1WYT|A Chain A, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Apo Form
pdb|1WYT|C Chain C, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Apo Form
pdb|1WYU|A Chain A, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|C Chain C, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|E Chain E, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|G Chain G, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYV|A Chain A, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|C Chain C, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|E Chain E, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|G Chain G, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
Length = 438
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 15/59 (25%)
Query: 331 NPTLMQTLEGTPVLVHAGPFANIAHGNSSI---VADKIALKLVGPGGIVVTEAGFGADI 386
NP + LE GPFA AHG ++ VAD ++L ++ P G +GADI
Sbjct: 204 NPNFLGALEDL------GPFAEAAHGAGALFVAVADPLSLGVLKPPG------AYGADI 250
>pdb|3OET|A Chain A, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|B Chain B, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|C Chain C, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|D Chain D, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|E Chain E, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|F Chain F, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|G Chain G, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
pdb|3OET|H Chain H, D-Erythronate-4-Phosphate Dehydrogenase Complexed With Nad
Length = 381
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 59 VLDELEGSADGYYVVVGEITRTPLGEGEITQYPLGEGKSTTTVGLCQALGAFLDKKVVTC 118
VLD EG D + V + +G I Y L EGK+ T + +A AF+ ++
Sbjct: 233 VLDVWEGEPD---LNVALLEAVDIGTSHIAGYTL-EGKARGTTQVFEAYSAFIGREQRVA 288
Query: 119 LRQPLQGPTFG 129
L L P FG
Sbjct: 289 LETLLPAPEFG 299
>pdb|1CC1|S Chain S, Crystal Structure Of A Reduced, Active Form Of The
Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum
Length = 283
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 6/86 (6%)
Query: 29 LHISEIAQELNLKPNH-YDLYGKYKAKVLLSVLDELEGSADGYYVVVGEITRTPLGEGEI 87
H + +A E + H Y++ K+ L V + + +G Y +VGE E+
Sbjct: 45 FHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKAHHHEV 104
Query: 88 TQYPL-----GEGKSTTTVGLCQALG 108
T L + +T VG C A G
Sbjct: 105 TMMELIRDLAPKSLATVAVGTCSAYG 130
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|B Chain B, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|B Chain B, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|B Chain B, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|B Chain B, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|B Chain B, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|B Chain B, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|B Chain B, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|B Chain B, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|B Chain B, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1224
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 217 KPEDLTPEEINRFARLDIDPA 237
+PEDL P E N LD+DPA
Sbjct: 706 QPEDLEPAEANEENDLDVDPA 726
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.137 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,181,047
Number of Sequences: 62578
Number of extensions: 452155
Number of successful extensions: 966
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 948
Number of HSP's gapped (non-prelim): 14
length of query: 400
length of database: 14,973,337
effective HSP length: 101
effective length of query: 299
effective length of database: 8,652,959
effective search space: 2587234741
effective search space used: 2587234741
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)